Address some mypy type hinting issues

src/quacc/atoms/slabs.py

@@ -201,7 +201,7 @@ def make_slabs_from_bulk(
         # Add slab to list
         slabs_with_props.append(slab)
 
-    final_slabs = []
+    final_slabs: list[Atoms] = []
     if not slabs_with_props:
         return final_slabs
 
@@ -224,7 +224,7 @@ def make_adsorbate_structures(
     atoms: Atoms,
     adsorbate: Atoms,
     min_distance: float = 2.0,
-    modes: list[str] | None = None,
+    modes: list[Literal["ontop", "bridge", "hollow", "subsurface"]] | None = None,
     allowed_surface_symbols: list[str] | None = None,
     allowed_surface_indices: list[int] | None = None,
     ads_site_finder_kwargs: AdsSiteFinderKwargs | None = None,
@@ -282,7 +282,7 @@ def make_adsorbate_structures(
         msg = "Cannot specify both modes and find_ads_sites_kwargs['positions']"
         raise ValueError(msg)
     find_ads_sites_kwargs["distance"] = min_distance
-    find_ads_sites_kwargs["positions"] = [mode.lower() for mode in modes]
+    find_ads_sites_kwargs["positions"] = modes
 
     # Check the provided surface indices are reasonable
     atom_indices = [atom.index for atom in atoms]

src/quacc/calculators/espresso/espresso.py

@@ -214,7 +214,7 @@ def read_results(self, directory: Path | str) -> dict[str, Any]:
         """
         results = {}
         if self.binary == "pw":
-            atoms = read(directory / self.outputname, format="espresso-out")
+            atoms = read(Path(directory) / self.outputname, format="espresso-out")
             results = dict(atoms.calc.properties())
         elif self.binary in ["ph", "phcg"]:
             with Path(directory, self.outputname).open() as fd:

src/quacc/calculators/vasp/vasp.py

@@ -281,7 +281,7 @@ def _cleanup_params(self) -> None:
 
     def _run(
         self,
-        command: list[str] | None = None,
+        command: str | None = None,
         out: Path | str | None = None,
         directory: Path | str | None = None,
     ) -> int:

src/quacc/calculators/vasp/vasp_custodian.py

@@ -156,7 +156,6 @@ def run_custodian(
     )
 
     # Handlers for VASP
-    handlers = []
     handlers_dict = {
         "VaspErrorHandler": VaspErrorHandler(vtst_fixes=vtst_fixes),
         "FrozenJobErrorHandler": FrozenJobErrorHandler(),

src/quacc/recipes/gulp/_base.py

@@ -79,6 +79,9 @@
             keyword_defaults += ["conv"]
         keyword_defaults = [k for k in keyword_defaults if k not in ["gwolf", "conp"]]
 
+    if option_defaults is None:
+        option_defaults = []
+
     option_defaults += [
         (
             f"output cif {GEOM_FILE_PBC}"

src/quacc/recipes/vasp/core.py

@@ -291,11 +291,12 @@ def non_scf_job(
         Dictionary of results from [quacc.schemas.vasp.vasp_summarize_run][].
         See the type-hint for the data structure.
     """
-    vasprun_path = zpath(Path(prev_dir, "vasprun.xml"))
+
+    vasprun_path = zpath(str(Path(prev_dir, "vasprun.xml")))
     vasprun = Vasprun(vasprun_path)
 
     prior_nbands = vasprun.parameters["NBANDS"]
-    calc_defaults = {
+    calc_defaults: dict[str, Any] = {
         "icharg": 11,
         "kspacing": None,
         "lcharg": False,

src/quacc/runners/prep.py

@@ -138,7 +138,7 @@ def calc_cleanup(
         symlink_path.unlink(missing_ok=True)
 
 
-def terminate(tmpdir: Path | str, exception: Exception) -> Exception:
+def terminate(tmpdir: Path | str, exception: Exception) -> None:
     """
     Terminate a calculation and move files to a failed directory.
 
@@ -149,11 +149,16 @@ def terminate(tmpdir: Path | str, exception: Exception) -> Exception:
     exception
         The exception that caused the calculation to fail.
 
+    Returns
+    -------
+    None
+
     Raises
     -------
     Exception
         The exception that caused the calculation to fail.
     """
+    tmpdir = Path(tmpdir)
     settings = get_settings()
     job_failed_dir = tmpdir.with_name(tmpdir.name.replace("tmp-", "failed-"))
     tmpdir.rename(job_failed_dir)

src/quacc/schemas/_aliases/cclib.py

@@ -89,8 +89,8 @@ class Attributes(TypedDict, total=False):
     natom: int
     nbasis: int
     nmo: int
-    nmrtensors: dict[int, dict[NDArray]]
-    nmrcouplingtensors: dict[int, dict[NDArray]]
+    nmrtensors: dict[int, dict[str, NDArray]]
+    nmrcouplingtensors: dict[int, dict[str, NDArray]]
     nocoeffs: NDArray
     nooccnos: NDArray
     nsocoeffs: list[NDArray]

src/quacc/schemas/vasp.py

@@ -125,8 +125,8 @@ def vasp_summarize_run(
         raise RuntimeError(
             f"VASP calculation did not converge. Will not store task data. Refer to {directory}"
         )
-
-    initial_atoms = read(zpath(directory / "POSCAR"))
+    poscar_path = directory / "POSCAR"
+    initial_atoms = read(zpath(str(poscar_path)))
     base_task_doc = summarize_run(
         final_atoms, initial_atoms, move_magmoms=move_magmoms, store=None
     )

src/quacc/utils/files.py

@@ -46,7 +46,8 @@ def check_logfile(logfile: str | Path, check_str: str) -> bool:
     bool
         True if the string is found in the logfile, False otherwise.
     """
-    zlog = Path(zpath(Path(logfile).expanduser()))
+    logfile_path = Path(logfile).expanduser()
+    zlog = Path(zpath(str(logfile_path)))
     with zopen(zlog, "r") as f:
         for line in f:
             clean_line = line if isinstance(line, str) else line.decode("utf-8")

src/quacc/utils/lists.py

@@ -25,8 +25,8 @@ def merge_list_params(
         Merged list
     """
     merged_list = []
-    lists = [list_ for list_ in lists if list_]
-    for list_ in lists:
+    lists_ = [list_ for list_ in lists if list_]
+    for list_ in lists_:
         for item in list_:
             item_ = item
             if case_insensitive:

src/quacc/wflow_tools/job_patterns.py

@@ -37,7 +37,7 @@ def map_partitioned_lists(
     func: Callable,
     num_partitions: int,
     unmapped_kwargs: dict[str, Any] | None = None,
-    **mapped_kwargs: dict[str, list[list[Any]]],
+    **mapped_kwargs: list[list[Any]],
 ) -> list[Any]:
     """
     Given list-of-lists parameters (say a list of batches that we want to map over),